Some of our users upgraded their devices to 88xx models. Is there a way to disable PTT, Shop Tunes, and other applications on devices via IT policy? Also I tried to uninstall manually through desktop manager and it does not appear. I know it is probably links on the phone not actually applications, but would like to disable those features.

Yes you can. Search the forum for "Policy Reference Guide" ... it'll give you a list of every IT Policy setting and what they do. If you want to allow some applications but not others you'll need to create an application control policy where you'd explicitly allow them.

You can delete the application from the handheld by going to options > applications and deleting them from the list.